Java tutorial
/* * Copyright 2015 OpenCB * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package org.opencb.cellbase.lib.impl; import com.mongodb.BasicDBList; import com.mongodb.QueryBuilder; import com.mongodb.client.model.Filters; import org.bson.Document; import org.bson.conversions.Bson; import org.opencb.biodata.models.core.Region; import org.opencb.biodata.models.variant.avro.Score; import org.opencb.cellbase.core.api.ConservationDBAdaptor; import org.opencb.biodata.models.core.GenomicScoreRegion; import org.opencb.cellbase.lib.MongoDBCollectionConfiguration; import org.opencb.commons.datastore.core.Query; import org.opencb.commons.datastore.core.QueryOptions; import org.opencb.commons.datastore.core.QueryResult; import org.opencb.commons.datastore.mongodb.MongoDataStore; import java.util.*; import java.util.function.Consumer; /** * Created by swaathi on 26/11/15. */ @Deprecated public class ConservationMongoDBAdaptor extends MongoDBAdaptor implements ConservationDBAdaptor { public ConservationMongoDBAdaptor(String species, String assembly, MongoDataStore mongoDataStore) { super(species, assembly, mongoDataStore); mongoDBCollection = mongoDataStore.getCollection("conservation"); logger.debug("ConservationMongoDBAdaptor: in 'constructor'"); } @Override public QueryResult<Long> update(List objectList, String field, String[] innerFields) { return null; } @Override public QueryResult<Long> count(Query query) { Bson bson = parseQuery(query); return mongoDBCollection.count(bson); } @Override public QueryResult distinct(Query query, String field) { Bson bson = parseQuery(query); return mongoDBCollection.distinct(field, bson); } @Override public QueryResult stats(Query query) { return null; } @Override public QueryResult get(Query query, QueryOptions options) { return null; } @Override public QueryResult nativeGet(Query query, QueryOptions options) { Bson bson = parseQuery(query); return mongoDBCollection.find(bson, options); } @Override public Iterator iterator(Query query, QueryOptions options) { return null; } @Override public Iterator nativeIterator(Query query, QueryOptions options) { Bson bson = parseQuery(query); return mongoDBCollection.nativeQuery().find(bson, options).iterator(); } @Override public QueryResult rank(Query query, String field, int numResults, boolean asc) { return null; } @Override public QueryResult groupBy(Query query, String field, QueryOptions options) { return null; } @Override public QueryResult groupBy(Query query, List fields, QueryOptions options) { return null; } @Override public void forEach(Query query, Consumer action, QueryOptions options) { } private Bson parseQuery(Query query) { List<Bson> andBsonList = new ArrayList<>(); createRegionQuery(query, ConservationDBAdaptor.QueryParams.REGION.key(), andBsonList); if (andBsonList.size() > 0) { return Filters.and(andBsonList); } else { return new Document(); } } // @Override public List<QueryResult> getAllByRegionList(List regionList, QueryOptions options) { //TODO not finished yet List<Document> queries = new ArrayList<>(); List<String> ids = new ArrayList<>(regionList.size()); List<String> integerChunkIds; List<Region> regions = regionList; for (Region region : regions) { integerChunkIds = new ArrayList<>(); // positions below 1 are not allowed if (region.getStart() < 1) { region.setStart(1); } if (region.getEnd() < 1) { region.setEnd(1); } // Max region size is 10000bp if (region.getEnd() - region.getStart() > 10000) { region.setEnd(region.getStart() + 10000); } QueryBuilder builder; int regionChunkStart = getChunkId(region.getStart(), MongoDBCollectionConfiguration.CONSERVATION_CHUNK_SIZE); int regionChunkEnd = getChunkId(region.getEnd(), MongoDBCollectionConfiguration.CONSERVATION_CHUNK_SIZE); if (regionChunkStart == regionChunkEnd) { builder = QueryBuilder.start("_chunkIds").is(getChunkIdPrefix(region.getChromosome(), region.getStart(), MongoDBCollectionConfiguration.CONSERVATION_CHUNK_SIZE)); } else { // for (int chunkId = regionChunkStart; chunkId <= regionChunkEnd; chunkId++) { //// integerChunkIds.add(chunkId); // integerChunkIds.add(region.getChromosomeInfo() + "_" + chunkId + "_" + this.chunkSize/1000 + "k"); // } // builder = QueryBuilder.start("chromosome").is(region.getChromosomeInfo()).and("chunkId").in(integerChunkIds); builder = QueryBuilder.start("chromosome").is(region.getChromosome()).and("end") .greaterThanEquals(region.getStart()).and("start").lessThanEquals(region.getEnd()); } // QueryBuilder builder = QueryBuilder.start("chromosome").is(region.getChromosomeInfo()).and("chunkId").in(hunkIds); /****/ queries.add(new Document(builder.get().toMap())); ids.add(region.toString()); // logger.debug(builder.get().toString()); } List<QueryResult> queryResults = executeQueryList2(ids, queries, options); for (int i = 0; i < regions.size(); i++) { Region region = regions.get(i); QueryResult queryResult = queryResults.get(i); // BasicDBList list = (BasicDBList) queryResult.getResult(); List list = queryResult.getResult(); Map<String, List<Float>> typeMap = new HashMap<>(); // int start = region.getStart(); for (int j = 0; j < list.size(); j++) { Document chunk = (Document) list.get(j); String source = chunk.getString("source"); List<Float> valuesList; if (!typeMap.containsKey(source)) { valuesList = new ArrayList<>(region.getEnd() - region.getStart() + 1); for (int val = 0; val < region.getEnd() - region.getStart() + 1; val++) { valuesList.add(null); } typeMap.put(source, valuesList); } else { valuesList = typeMap.get(source); } // BasicDBList valuesChunk = (BasicDBList) chunk.get("values"); ArrayList valuesChunk = chunk.get("values", ArrayList.class); int pos = 0; if (region.getStart() > chunk.getInteger("start")) { pos = region.getStart() - chunk.getInteger("start"); } for (; pos < valuesChunk.size() && (pos + chunk.getInteger("start") <= region.getEnd()); pos++) { // System.out.println("valuesList SIZE = " + valuesList.size()); // System.out.println("pos = " + pos); // System.out.println("DIV " + (chunk.getInt("start") - region.getStart())); // System.out.println("valuesChunk = " + valuesChunk.get(pos)); // System.out.println("indexFinal = " + (pos + chunk.getInt("start") - region.getStart())); valuesList.set(pos + chunk.getInteger("start") - region.getStart(), new Float((Double) valuesChunk.get(pos))); } } // BasicDBList resultList = new BasicDBList(); // ConservationScoreRegion conservedRegionChunk; GenomicScoreRegion<Float> conservedRegionChunk; for (Map.Entry<String, List<Float>> elem : typeMap.entrySet()) { // conservedRegionChunk = new ConservationScoreRegion(region.getChromosome(), region.getStart(), // region.getEnd(), elem.getKey(), elem.getValue()); conservedRegionChunk = new GenomicScoreRegion<>(region.getChromosome(), region.getStart(), region.getEnd(), elem.getKey(), elem.getValue()); resultList.add(conservedRegionChunk); } queryResult.setResult(resultList); } return queryResults; } @Override @Deprecated public List<QueryResult> getAllScoresByRegionList(List regionList, QueryOptions options) { //TODO not finished yet List<Document> queries = new ArrayList<>(); List<String> ids = new ArrayList<>(regionList.size()); List<Integer> integerChunkIds; List<Region> regions = regionList; for (Region region : regions) { integerChunkIds = new ArrayList<>(); // positions below 1 are not allowed if (region.getStart() < 1) { region.setStart(1); } if (region.getEnd() < 1) { region.setEnd(1); } /****/ QueryBuilder builder; int regionChunkStart = getChunkId(region.getStart(), MongoDBCollectionConfiguration.CONSERVATION_CHUNK_SIZE); int regionChunkEnd = getChunkId(region.getEnd(), MongoDBCollectionConfiguration.CONSERVATION_CHUNK_SIZE); if (regionChunkStart == regionChunkEnd) { builder = QueryBuilder.start("_chunkIds").is(getChunkIdPrefix(region.getChromosome(), region.getStart(), MongoDBCollectionConfiguration.CONSERVATION_CHUNK_SIZE)); } else { // for (int chunkId = regionChunkStart; chunkId <= regionChunkEnd; chunkId++) { // integerChunkIds.add(chunkId); // } // // QueryBuilder builder = QueryBuilder.start("chromosome").is(region.getChromosomeInfo()).and("chunkId").in(hunkIds); // builder = QueryBuilder.start("chromosome").is(region.getChromosomeInfo()).and("chunkId").in(integerChunkIds); builder = QueryBuilder.start("chromosome").is(region.getChromosome()).and("end") .greaterThanEquals(region.getStart()).and("start").lessThanEquals(region.getEnd()); } /****/ queries.add(new Document(builder.get().toMap())); ids.add(region.toString()); // logger.debug(builder.get().toString()); } List<QueryResult> queryResults = executeQueryList2(ids, queries, options); // List<QueryResult> queryResults = executeQueryList(ids, queries, options); for (int i = 0; i < regions.size(); i++) { Region region = regions.get(i); QueryResult queryResult = queryResults.get(i); List<Document> list = (List<Document>) queryResult.getResult(); Map<String, List<Float>> typeMap = new HashMap(); // int start = region.getStart(); for (int j = 0; j < list.size(); j++) { Document chunk = list.get(j); if (!chunk.isEmpty()) { // BasicDBList valuesChunk = (BasicDBList) chunk.get("values"); ArrayList valuesChunk = chunk.get("values", ArrayList.class); if (valuesChunk != null) { // TODO: temporary patch to skip empty chunks - remove as soon as conservation is reloaded String source = chunk.getString("source"); List<Float> valuesList; if (!typeMap.containsKey(source)) { valuesList = new ArrayList<>(region.getEnd() - region.getStart() + 1); for (int val = 0; val < region.getEnd() - region.getStart() + 1; val++) { valuesList.add(null); } typeMap.put(source, valuesList); } else { valuesList = typeMap.get(source); } // valuesChunk = (BasicDBList) chunk.get("values"); valuesChunk = chunk.get("values", ArrayList.class); int pos = 0; if (region.getStart() > chunk.getInteger("start")) { pos = region.getStart() - chunk.getInteger("start"); } for (; pos < valuesChunk.size() && (pos + chunk.getInteger("start") <= region.getEnd()); pos++) { valuesList.set(pos + chunk.getInteger("start") - region.getStart(), new Float((Double) valuesChunk.get(pos))); } } else { continue; } } BasicDBList resultList = new BasicDBList(); for (Map.Entry<String, List<Float>> elem : typeMap.entrySet()) { for (Float value : elem.getValue()) { if (value != null) { resultList.add(new Score(new Double(value), elem.getKey(), null)); } } } if (!resultList.isEmpty()) { queryResult.setResult(resultList); } else { queryResult.setResult(null); } } } return queryResults; } }